He is currently at Watford in the role of Head of Technical Development[3] and has also coached at Nottingham Forest, Wimbledon, Milton Keynes Dons and with The FA.
In October 1982, he joined Lincoln City on loan for one month in an attempt to gain first-team experience, but made only three substitute appearances during a spell he later described as "disappointing".
Gilligan failed to fire for the Red Imps, scoring a solitary goal as Lincoln slipped to relegation from the Football League.
In July 2001, following Platt's departure and the appointment of Paul Hart to the manager's position, Gilligan left his role at Nottingham Forest.
[11] He joined the PFA as a regional coach educator, whilst also helping out David Platt with the England U21s, before being appointed technical director at Wimbledon in February 2003.
[17] Gilligan remained in charge of the Nike Academy for three seasons, and is widely credited with discovering and developing players who have gone on to play at the FIFA World Cup, such as Tom Rogic and Seon-Min Moon.
Gilligan and his team scouted and coached over 130 players, out of whom 40 made it from amateur level to professional during this period, including Abdul Waris, David Accam, Petar Golubovic, Anfernee Dijksteel, Jorge Grant, Kevin Salazar and others.
[18] During this period, Gilligan's coaching methods and motivational half-time talks gained publicity in media such a FourFourTwo magazine.
In June 2019, he gained the UEFA Pro License, the highest coaching qualification, from The FA, having completed the course alongside Steven Gerrard and Peter Schmeichel.